Synthesis and Characterization of Oligodeoxynucleotides Containing Formamidopyrimidine Lesions and Nonhydrolyzable Analogues

Haraguchi, Kazuhiro; Delaney, Michael O.; Wiederholt, Carissa J.; Sambandam, Aruna; Hantosi, Zsolt; Greenberg, Marc M.

doi:10.1021/ja012135q

Cited by 103 publications

(108 citation statements)

References 44 publications

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“…The major lesions observed to date with riboflavin consist of Fpg-sensitive 8-oxo-G and piperidine-sensitive Ox (39, 40, 68 -70), along with smaller amounts of spiroiminodihydantoin, which is sensitive to Fpg (46,71) and partially labile in piperidine (47). The major stable G oxidation products in hydroxyl radical-induced DNA damage (7,72,73) include 8-oxo-G and Ox, along with Fapy-G, which is sensitive to both Fpg and piperidine (40). The ϳ2-fold sequence-dependent variation in the proportions of Fpg-and piperidine-sensitive lesions produced by the hydroxyl radical generators and riboflavin is smaller than the ϳ5-fold range for ONOOCO 2 Ϫ -induced G oxidation (28) and points to the modest role of sequence context in determining the spectrum of G damage products.…”

Section: Discussionmentioning

confidence: 99%

DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants

Margolin

Shafirovich

Geacintov

et al. 2008

Journal of Biological Chemistry

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DNA sequence context has emerged as a critical determinant of the location and quantity of nucleobase damage caused by many oxidizing agents. However, the complexity of nucleobase and 2-deoxyribose damage caused by strong oxidants such as ionizing radiation and the Fenton chemistry of Fe 2؉ -EDTA/ H 2 O 2 poses a challenge to defining the location of nucleobase damage and the effects of sequence context on damage chemistry in DNA. To address this problem, we developed a gel-based method that allows quantification of nucleobase damage in oxidized DNA by exploiting Escherichia coli exonuclease III to remove fragments containing direct strand breaks and abasic sites. The rigor of the method was verified in studies of guanine oxidation by photooxidized riboflavin and nitrosoperoxycarbonate, for which different effects of sequence context have been demonstrated by other approaches (Margolin, Y., Cloutier, J. F., Shafirovich, V., Geacintov, N. E., and Dedon, P. C. (2006) Nat. Chem. Biol. 2, 365-366). Using duplex oligodeoxynucleotides containing all possible three-nucleotide sequence contexts for guanine, the method was used to assess the role of DNA sequence context in hydroxyl radical-induced guanine oxidation associated with ␥-radiation and Fe 2؉ -EDTA/H 2 O 2 . The results revealed both differences and similarities for G oxidation by hydroxyl radicals and by one-electron oxidation by riboflavin-mediated photooxidation, which is consistent with the predominance of oxidation pathways for hydroxyl radicals other than one-electron oxidation to form guanine radical cations. Although the relative quantities of G oxidation produced by hydroxyl radicals were more weakly correlated with sequencespecific ionization potential than G oxidation produced by riboflavin, damage produced by both hydroxyl radical generators and riboflavin within two-and three-base runs of G showed biases in location that are consistent with a role for electron transfer in defining the location of the damage products. Furthermore, both ␥-radiation and Fe 2؉ -EDTA/H 2 O 2 showed relatively modest effects of sequence context on the proportions of different damage products sensitive to E. coli formamidopyrimidine DNA glycosylase and hot piperidine, although GT-containing sequence contexts displayed subtle biases in damage chemistry (formamidopyrimidine DNA glycosylase/piperidine ratio). Overall, the results are consistent with the known chemistry of guanine oxidation by hydroxyl radical and demonstrate that charge migration plays a relatively minor role in determining the location and chemistry of hydroxyl radical-mediated oxidative damage to guanine in DNA.With implications for mutagenesis and carcinogenesis, DNA damage caused by strong oxidizing agents such as ionizing radiation and Fenton chemistry (e.g. Fe 2ϩ -EDTA, Cu ϩ /H 2 O 2 ) affects both the base and sugar moieties (1, 2). This complexity poses a challenge to understanding the mechanisms of formation of the ultimate stable oxidation products and their relative amounts, especially in terms of...

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Section: Discussionmentioning

confidence: 99%

DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants

Margolin

Shafirovich

Geacintov

et al. 2008

Journal of Biological Chemistry

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“…FapyG-or FapyA-containing oligonucleotides were synthesized as described previously (17,18). The oligonucleotides were characterized by electrospray ionization mass spectroscopy, and the spectra showing the expected fragment masses are presented in Supplemental Fig.…”

Section: Methodsmentioning

confidence: 99%

“…A method for the synthesis of oligonucleotides containing FapyG and FapyA at defined sites was recently developed (17,18). Here, we have reported the first study of the repair of FapyG and FapyA in these oligonucleotides, using nuclear and mitochondrial extracts of wild type and mice deficient in the two major glycosylases for the repair of oxidative DNA damage, OGG1 and NTH1.…”

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confidence: 99%

Repair of Formamidopyrimidines in DNA Involves Different Glycosylases

Souza-Pinto

Haraguchi

et al. 2005

Journal of Biological Chemistry

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The oxidatively induced DNA lesions 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA) are formed abundantly in DNA of cultured cells or tissues exposed to ionizing radiation or to other free radical-generating systems. In vitro studies indicate that these lesions are miscoding, can block the progression of DNA polymerases, and are substrates for base excision repair. However, no study has yet addressed how these lesions are metabolized in cellular extracts. The synthesis of oligonucleotides containing FapyG and FapyA at defined positions was recently reported. These constructs allowed us to investigate the repair of Fapy lesions in nuclear and mitochondrial extracts from wild type and knock-out mice lacking the two major DNA glycosylases for repair of oxidative DNA damage, OGG1 and NTH1. The background level of FapyG/FapyA in DNA from these mice was also determined. Endogenous FapyG levels in liver DNA from wild type mice were significantly higher than 8-hydroxyguanine levels. FapyG and FapyA were efficiently repaired in nuclear and mitochondrial extracts from wild type animals but not in the glycosylasedeficient mice. Our results indicated that OGG1 and NTH1 are the major DNA glycosylases for the removal of FapyG and FapyA, respectively. Tissue-specific analysis suggested that other DNA glycosylases may contribute to FapyA repair when NTH1 is poorly expressed. We identified NEIL1 in liver mitochondria, which could account for the residual incision activity in the absence of OGG1 and NTH1. FapyG and FapyA levels were significantly elevated in DNA from the knock-out mice, underscoring the biological role of OGG1 and NTH1 in the repair of these lesions.A large number of DNA base modifications are formed by oxidative damage to DNA (for review, see Ref. 1). Some of these lesions are generated at high rates, even in the absence of exogenous DNA-damaging agents. For instance, it was estimated that 100 -500 8-hydroxyguanines 3 are formed per day in a human cell (2). 8-oxoG is one of the most studied DNA lesions, and it is often used as a biomarker of oxidative DNA damage. However, ring-opened formamidopyrimidine lesions, 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 4,6-diamino-5-formamidopyrimidine (FapyA), are formed at equal or higher levels than 8-oxoG after oxidative stress (3-5). These lesions result from hydroxyl radical attack on guanine and adenine, respectively, followed by one-electron reduction of the hydroxyl adduct radicals (1), which are also intermediates in the formation of 8-oxoG and 8-oxoA (6). Formation of Fapy lesions in DNA upon UV radiation has also been reported (7). FapyA (8) and FapyG (9) are miscoding in vitro, both directing the preferential misincorporation of adenine opposite the lesions by a bacterial DNA polymerase (Klenow exo Ϫ ). Experiments using the methylated analogue of FapyG, i.e. 2,6-diamino-4-hydroxy-5-Nmethylformamidopyrimidine (Me-FapyG), have suggested that formamidopyrimidines might also constitute blocks to DNA poly...

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“…Decrease of thermal stability of Fapy-7MeG paired with C equals -3.9 o C, which is comparable to that caused by 8-oxoG:C pair (-3.5 o C) (Asagoshi et al, 2002). Presence of unsubstituted FapyA and FapyG also decreases melting points of duplexes by 1-7 o C, depending on the opposite base in the complementary strain, with the exception of FapyG:A mismatch, which melts higher than G:A duplex (Haraguchi et al, 2002). FapyG with a bulky adduct of aflatoxin B 1 changes markedly the structure of DNA duplex, but differently than its precursor G-AFB 1 adducts (Smela et al, 2002).…”

Section: Introductionmentioning

confidence: 98%

Imidazole Ring-Opened DNA Purines and Their Biological Significance

Tudek¹

2003

BMB Reports

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Synthesis and Characterization of Oligodeoxynucleotides Containing Formamidopyrimidine Lesions and Nonhydrolyzable Analogues

Cited by 103 publications

References 44 publications

DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants

DNA Sequence Context as a Determinant of the Quantity and Chemistry of Guanine Oxidation Produced by Hydroxyl Radicals and One-electron Oxidants

Repair of Formamidopyrimidines in DNA Involves Different Glycosylases

Imidazole Ring-Opened DNA Purines and Their Biological Significance

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